Globin Gene Research Articles

Association of alpha globin gene copy number with exhaled nitric oxide in a cross-sectional study of healthy Black adults

IntroductionThe genetic determinants of fractional exhalation of nitric oxide (FeNO), a marker of lung inflammation, are understudied in Black individuals. Alpha globin (HBA) restricts nitric oxide signalling in arterial endothelial...

Functional characterization of compound heterozygosity Hb S/Hb Deer Lodge in Brazil

IntroductionThe Hb Deer Lodge (β2 His>Arg; HBB:c.8A>G) is a structural hemoglobin variant described in some populations around the world, characterized by increased oxygen affinity, but does not confer clinical symptoms to its carriers. The coinheritance of the Hb Deer Lodge with the most common hemoglobin variant, Hb S, has been reported only once; however, functional data were not described. Here we show a case of the Hb S and Hb Deer Lodge carrier in heterozygosity. MethodsThe Hb S and Hb Deer Lodge association was identified by High-Performance Liquid Chromatography (HPLC), reverse phase HPLC and the β globin gene sequencing. The functional characterization of this interaction was obtained using the O2 dissociation curve, determination of the cooperativity between the globin chains and the Bohr effect in the presence and absence of organic phosphates. ResultsWhen the Hb S and Hb Deer Lodge were associated, there was a decrease in cooperativity, no significant changes in oxygen affinity and no significant Bohr effect changes. ConclusionDespite these genetic variations, the carrier showed no hematological alterations and no clinical symptoms, possibly due to the high oxygen affinity of the Hb Deer Lodge, which interferes with the Hb S polymerization.

Iron-Overload Conditions: Manifestations to the Kidney Organs – A Review

Excess iron is a risk factor for organ dysfunction and damage resulting in various organ diseases such as liver, heart, and kidney, diabetes mellitus, and neurodegenerative diseases. Iron overload in some individuals is caused by various factors, including genetic predisposition such as genetic hemochromatosis, repeated transfusion of red blood cells, and parenteral iron administration in conditions of transfusion-dependent anemia. A disturbance in the globin gene in diseases such as β-thalassemia major causes an imbalance of the globin chain, resulting in chronic anemia in the sufferer. It has been reported that the human body does not have a mechanism for eliminating excess iron levels. Routine transfusion has become a solution to overcome chronic anemia so that patients can maintain hemoglobin levels, and the result of this transfusion repetition is the accumulation of iron in various organs, such as the heart, liver, endocrine glands, pancreas, lungs, and kidneys. Excess iron can be toxic to the body due to the formation of harmful free radicals that can damage cells and tissues. An increase in excessive ROS can result in the saturation of the antioxidant system. The presence of free radicals can lead to damage and the occurrence of filtration dysfunction in the glomerulus.

Identification of Hb Lepore, Hb anti-Lepore, and α-globin gene triplications by long-read single-molecule real-time sequencing.

Hemoglobin (Hb) Lepore and Hb anti-Lepore are infrequent fusion gene variants that result from nonhomologous crossovers during meiosis. Conventional molecular testing methods may face challenges in identifying these variants. During Hb analysis using capillary electrophoresis, we encountered 6 cases with unusual Hb variants. Our aim was to identify the alterations in their globin genes. Gap-polymerase chain reaction (PCR), reverse dot-blot assay (RDB), Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and long-read single-molecule real-time (SMRT) sequencing were used to confirm the presence of globin gene alterations. The routine thalassemia gene test kit using the gap-PCR and RDB techniques did not detect common gene variations. Direct sequencing failed to identify any known or unknown globin gene alterations. The MLPA analysis, however, revealed the possible presence of α-globin gene triplications as well as 2 types of fusion gene alterations. Further analysis using long-read SMRT sequencing accurately identified 3 rare gene variations: αααanti-3.7, Hb Lepore-Boston-Washington, and Hb anti-Lepore P-India. Conventional methods may overlook rare thalassemias or Hb variants. Long-read SMRT sequencing has the potential to identify breakpoints in fusion genes, demonstrating that it is a promising technique for detecting rare thalassemias.

Sir David John Weatherall. 9 March 1933—8 December 2018

Sir David Weatherall was the outstanding, internationally recognized, clinician scientist of his generation. His lifelong interest in the haemoglobinopathies first came from studying a child that he recognized as having beta thalassaemia while working as an army physician in Malaya. His interest in these diseases further developed as he undertook his PhD in the Department of Haematology under the supervision of Lockard Conley and Victor McKusick in Baltimore. There, together with John Clegg (FRS 1999), he developed the technology to directly measure the synthesis of the alpha and beta globin chains of haemoglobin, and his subsequent work at the University of Liverpool showed that thalassaemia resulted from imbalanced globin chain synthesis. Importantly, using the globin genes as their model, David's laboratory went on to make many of the first discoveries of how expression of the globin genes and mammalian genes in general could be perturbed to cause human genetic diseases. As professor of medicine in Oxford, he established one of the first institutes to develop the use of molecular biology in medicine and he trained many of the world's leading clinician scientists in this area of biomedical research. He also established worldwide networks to apply molecular biology to the haemoglobinopathies and infectious diseases, making a unique contribution to global medicine. He had outstanding qualities as a clinician, a scientist, and a leader, all of which he achieved with great humility and humanity.

A rare case of compound Hemoglobin Lansing/Hemoglobin S coinherited with alpha thalassemia trait (-alpha3.7) presented with spurious hypoxemia and moderate hemolytic anemia

Abstract We present a case of a 27-year-old female at 27 weeks of gestation, who presented at the emergency department for vaginal spotting. She was also found to have low oxygenation on pulse oximetry of approximately 82% at room air. Her SpO2 did not improve with O2 supplement. She had a similar presentation a month before, with mild light-headedness and low oxygenation. However, two repeated air blood gas (ABG) findings were normal for oxygen saturation. Hemoglobinopathy was suspected due to the disparity. She was anemic during her presentation, with hemoglobin 8.3 g/dl, RBC count 3.36 million/ul, MCV 81 fl and MCH 24.7 pg. Additional workup showed increased reticulocyte count, decreased haptoglobin, negative direct Coombs test, negative G6PD test, and no evidence of a PNH clone. Capillary hemoglobin electrophoresis showed HbA 59.8%, HbS 34.5%, HbA2 3.6% and a small peak (2.1%) in the Z8 zone with a trailing edge at HbF window. HPLC revealed an “unknown peak” of 8.2% with a retention time of 1.93 minutes as well as the HbS peak. There was also a tiny additional A2 peak unresolved from the main A2 peak. Alpha globin gene sequencing revealed one copy of the -alpha3.7 alpha-globin deletion and one copy of Hb Lansing variant in the alpha2-globin gene. This is consistent with the compound Hemoglobin Lansing/Hemoglobin S coinherited with alpha thalassemia trait. Hemoglobin Lansing is a rare unstable alpha hemoglobin variant with mutation of c.264C>G resulting with a substitution of His by Gln at codon 87. The mutation was first discovered in the alpha 2 gene. Then the same mutation was found in alpha 1 gene later and named as Hemoglobin Lansing-Ramathibodi. To the best of our knowledge, this is the first reported case of Hemoglobin Lansing with alpha thalassemia trait (-alpha3.7) and HbS. Spuriously low pulse oximetry measurements have previously been reported in Hb Lansing variants. It was speculated to be due to different absorption spectra of Hb Lansing which is under study now. The patient also presented with hemolytic anemia. The exact cause was undetermined yet although it might be related to her hemoglobinopathy. Mild hemolytic anemia was reported in two cases of co-inheritance of Lansing-Ramathibodi and Hb Pakse (a non-deletional alpha thalassemia) but not in the members of the same family with Hb Lansing alone. It was also reported that some unstable alpha chain variants, when associated with another alpha thalassemia defect, present with a more severe phenotype including hemolytic anemia even though essentially asymptomatic in a heterozygous state.

Is Epigenetic Modulation to Induce Fetal Hemoglobin Translatable in Sickle Cell Mice?

Sickle cell disease (SCD) is a genetic disorder caused by a mutation in the β-globin subunit of hemoglobin, resulting in the formation of HbS. Under deoxygenation, HbS polymerizes leading to red blood cell sickling, increased hemolysis and multi-organ damage. During human fetal development, due to expression of the γ-globin gene, the predominant type of hemoglobin produced is fetal hemoglobin (HbF). However, after birth, this shifts to adult globin (HbA or HbS in SCD). This is driven by epigenetic repression of γ-globin due to an increased methylation of its gene promoters. DNA methyltransferase 1 (DNMT1) is an important enzyme for DNA methylation and is known to be pivotal in regulation of HbF expression. Reactivation of HbF provides a functional hemoglobin, and therefore has the potential to treat SCD symptoms ( Steinberg et al. JAMA 2003;289:1645-51). HbF induction is an accepted treatment strategy in SCD; even small increases result in decreased vaso-occlusive crises and mortality ( Kato et al. Nat Rev Dis Primers 2018;4:18010). Decitabine inhibits DNMT1 activity, thus promoting γ-globin expression and thereby increasing HbF levels. While inhibition of DNA methylation is known to cause HbF induction in humans and non-human primates, the effects observed in SCD mouse models are more ambiguous. This study investigated to which extent decitabine treatment could induce HbF expression in the Townes SCD model. In Townes mice, the murine globin genes have been substituted for their sickle human counterparts, HBA, HBB sickle and HBG1, and mimic many features of human SCD. Mice aged 4-5 weeks were dosed subcutaneously 3 times a week for 12 weeks with research-grade decitabine (0.6 mg/kg or 0.4 mg/kg) or vehicle. Blood samples were collected for analysis of HbF protein levels by HPLC (represented as % of total Hb) and F-cells by flow cytometry (represented as % of the total RBC population positive for HbF), complete blood counts, histology, and other markers of disease and organ damage. Results are presented as mean ± SD. Groups were compared using an ANCOVA model, adjusting for multiple comparisons (Dunnett) with p<0.05 considered statistically significant. For both treatment groups, HbF was significantly elevated compared to the control group, with the maximal response observed at 12 weeks (Figure 1). F-cells at the end of the study were increased in both 0.4 mg/kg (11.4±1.5%) and 0.6 mg/kg (11.8±1.4%) groups compared to vehicle (4.5±0.6%). The same was observed for protein levels: 0.4 mg/kg group (1.2±0.3%), 0.6 mg/kg (1.4±0.3%) compared to vehicle (0.4±0.1%). Interestingly, after 12 weeks RBC and reticulocyte counts were significantly decreased in treatment groups and mean corpuscular volume (MCV) was significantly increased. No changes on LDH, bilirubin and liver markers (ALP, ALT, AST) were observed at 6 or 12 weeks. The results showed that treatment groups had significantly higher HbF levels than the vehicle group. However, the level of induction was lower than observed for inhibition of DNA methylation in humans and primates. The decrease in RBCs and reticulocytes could be partially explained by a combination of HbF induction, reduction of sickle RBC, and inhibition of erythropoiesis. The lack of changes in disease markers suggests that the increase in HbF levels in Townes mice might not be sufficient to alleviate the disease. This observation is consistent with recently published data (Woodard et al. Dis Model Mech. 2022;15(6)) that indicates that Townes mice are less suitable for studying this mechanism of action since, even though they have all human globin genes and some proximal regulatory elements, they lack key cis-acting distant DNA elements that regulate the globin genes. However, in primates the globin structure and regulation mechanisms are similar to human (Hardison. Cold Spring Harb Perspect Med. 2012;2(12)). In conclusion, although the measured levels of HbF protein were no higher than 2%, we found that decitabine can induce HbF expression in the Townes mouse model of SCD. However, within the 12-weeks, there was no clear beneficial effect on the disease markers studied. The successful induction of HbF suggests that better outcomes might be achieved with further optimization of the dosing and duration of the study. This indicates that SCD mice may be useful for preclinical studies of HbF induction, but caution is needed when extrapolating results to humans.

New Insights into Cellular Defects during Haematopoiesis of Sickle Cell Disease Using the Townes Mouse Model

Sickle cell disease (SCD) is an inherited disorder caused by a point mutation in the β globin gene leading to the synthesis of an abnormal haemoglobin (HbS), that under low oxygen tension polymerises driving the sickling of red blood cells and reducing their lifespan. SCD is characterized by anaemia, vaso-occlusion and haemolysis, progressive multiorgan damage and increased mortality. For decades, peripheral haemolysis has been considered as the sole driver of anaemia in SCD. Recently, we have demonstrated the occurrence of ineffective erythropoiesis (IE) in SCD suggesting that anaemia can be impacted by defects of central origin and hinting to abnormalities in the haematopoietic compartment. To gain insight into SCD haematopoiesis, we investigated the haematopoietic compartment of the humanized transgenic Townes mouse model by conducting an in-depth flow cytometry-based analysis in the bone marrow (BM) and spleen, comparing SS mice to control littermates (AA and AS) at 8 and 16 weeks of age (termed 8-w and 16-w, respectively). BM and spleen are two key hematopoietic tissues in adult mice: BM is involved in maintaining homeostatic haematopoiesis and spleen responds to stress haematopoiesis. First, we assessed haematopoietic differentiation in the BM of SS, AA and AS mice. Total number of BM cells and frequency of Lin Neg and Lin NegKit Pos (LK) were identical between SS and control littermates whereas a minor increase in the percentages of Lin NegSca PosKit Pos (LSK) was observed in 16-w SS mice. Within the LSK compartment, we found a 1.81- and 2.5-fold reduction of long-term haematopoietic stem cell (lt-HSC) frequency in 8-w and 16-w SS mice, respectively (Fig1 A). HSCs differentiate into multipotent progenitors (MPPs), which have decreased self-renewal capacity and progressively engage in the megakaryocytic (MPP2), myeloid-biased (MPP3), or lymphoid-biased (MPP4) lineage. The MPP3 compartment showed a 1.6-fold increased frequency in 8-w and 16-w SS mice indicating a skewing toward myeloid cell production and the onset of extramedullary haematopoiesis as early as 8 weeks after birth (Fig1 A). Next, we analysed the downstream lineages of the committed progenitors (lymphoid, granulo-macrophagic, megakaryocytic, and erythroid) and found a 1.4 and 2.3-fold increase of th megakaryocyte-erythroid progenitor cells (MEPs) and pre-CFU-Es in 8-w and 16-w SS mice, respectively (Fig1 A,B). We assessed the potential of SS hematopoietic progenitors (HSPCs) to differentiate into myelomonocytic and erythroid lineages by performing methylcellulose colony forming unit (CFU) assays with LSK and LK cells sorted from 8-w mice. Although no difference was observed in the number and type of colonies formed in vitro from SS and control HSPCs, SS colonies were much smaller than the AA/AS ones. Furthermore, serial replating showed a phenotype of stemness exhaustion in SS mice, with a dramatic decrease in the number of colonies formed by LSK cells (27.5 SS CFUs vs 51.6 AA/AS CFUs), suggesting lower self-renewal capacities of SS HSPCs. In spleen, in addition to the expected splenomegaly of SS mice, we found a trend toward a decreased frequency of the LSK compartment and an increase of the LK compartment. There was a 2.25- and 1.42-fold increase in the percentage of MPP-2 and MPP-3 cells, respectively, and a 2.1-fold increase in the pre-CFU-Es confirming an intense splenic haematopoiesis in SS mice (Fig 1B). HSPCs are known to be retained by the BM stromal cells through the chemotactic interaction of CXCL12 and CXCR4 and the adhesive interaction of VCAM-1 and VLA-4. Measuring HSC-related cytokines in BM supernatants, we found severely diminished levels of CXCL12 in SS mice as compared to control littermates (18 pg.mL -1 in SS vs 84 pg.mL -1 in AA; N=80), suggesting HSC mobilization from the BM to the spleen with disease onset. In addition to the well-established stress erythropoiesis phenotype reported in SCD mice, our study describes cellular abnormalities in the haematopoietic compartment shedding light on potential new mechanisms that contribute to SCD pathology in relation to anaemia and bone marrow stemness.

NR2F1 : A Novel Candidate for Gamma Globin Activation

The reactivation of human gamma globin holds tremendous promise as a potential treatment for hemoglobinopathies, including sickle cell disease and beta-thalassemia. Despite identifying various repressors of fetal globin genes in adult erythroid cells over the past decade, evidence concerning stage-specific factors that activate human fetal globin prior to the switch to adult beta-globin remains inadequately understood. In our study, we constructed an erythroid-specific gene regulatory network (GCN) by integrating multiple RNA-seq datasets from erythroid cells at different stages of differentiation and development. Our analysis unveiled both known HbF activators, like HIC2, and novel candidates. Among the novel contenders, NR2F1, a member of the steroid/thyroid hormone receptor superfamily, emerged as a prominent candidate. To validate our predictions, we overexpressed NR2F1 in Hudep2 cells and observed more than a four-fold increase (28% vs. 6%) in the proportion of F cells and a three-fold rise in HbF levels as measured by HPLC. In addition, the overexpression of NR2F1 did not appear to impact beta-globin expression or cell differentiation. Intriguingly, we observed a significant reduction in the protein level of BCL11A, a master regulator of HbF, despite no major change in the total RNA level of BCL11A. This observation suggests that NR2F1 plays a role in the post-transcriptional modification of BCL11A. Additionally, NR2F1 overexpression led to an upregulation of Lin28B expression in Hudep2 cells. Lin28B is known to directly bind BCL11A mRNA and prevent its effective translation without disturbing BCL11A transcription. Consequently, the observed upregulation of Lin28B in NR2F1-overexpressing cells implies a potential NR2F1-Lin28B-BCL11A axis involved in controlling human hemoglobin switching. In conclusion, our findings propose NR2F1 as a novel activator of gamma globin, representing an attractive target for gamma globin reactivation. Additional investigation is required to explore the molecular mechanisms through which NR2F1 regulates gamma globin expression and its role in the NR2F1-Lin28B-BCL11A axis.

Pyruvate Kinase Thermostability Is Associated with Red Blood Cell Adhesion, Deformability and Oxygen Affinity in Patients with Sickle Cell Disease

Introduction: Sickle cell disease(SCD) is caused by a mutation in the beta globin gene that causes formation of abnormal hemoglobin S (HbS). Red blood cells (RBCs) from patients with SCD are less deformable and take on the shape of sickle upon deoxygenation. This results in multiple downstream effects including RBC adhesion, microvascular occlusion and chronic hemolysis. RBCs rely solely on anaerobic glycolysis to produce adenosine triphosphate (ATP), which is needed to maintain the cell's structure and function. Pyruvate kinase (PK) is a key enzyme involved in the last step of glycolysis. We have previously demonstrated a decrease in PK activity and stability as a novel pathophysiological feature of SCD. Currently there are several clinical trials ongoing investigating the efficacy of PK activation by small molecules such as mitapivat (NL8517, NCT04000165, NCT05031780), AG-946 (NCT04536792) and etavopivat (NCT04624659, NCT04987489). In this study we aim to investigate how PK properties correlate to sickle RBC properties in order to explore if impaired PK function is associated with specific features of the complex SCD pathophysiology. Methods: Homozygous HbS (HbSS) and HbS/ β0 thalassemia patients were eligible to participate. Patients who received blood transfusion (<3 months) were excluded. Dense RBCs (MCHC >41 g/dL, Advia 120/2120 Siemens) and HbF and HbS levels (Tosoh G8) were measured. PK and hexokinase (HK) activity were measured on purified RBCs. PK thermostability (reflected by % residual PK activity) was measured on purified RBCs lysates after one hour of incubation (53°C). RBC adhesion to laminin (Biolamina) was measured using a microfluidic device (IBIDI µ-Slide I 0.4). RBC hydration (Ohyper), RBC deformability (EImax) and point of sickling (PoS) were assessed by osmotic and oxygen gradient ektacytometry using the Laser-Optical Rotational Red Cell Analyzer (Lorrca, RR Mechatronics). Oxygen affinity (P50) was measured with the Hemox-Analyzer (TCS). Statistical analysis was performed in Graphpad Prism (Pearson's correlation). Results: Fifty-seven patients with SCD (53 HbSS, 4 HbS/β 0 thalassemia) were included of which 17 were children (median age 14 years [range 6-17]) and 40 were adults (median age 36 years [range 18-58]). Baseline characteristics are depicted in Table 1. Figure 1 shows a heatmap with correlation coefficients of all laboratory parameters from Table 1 as measured in this cohort. When focusing on PK properties we found that patients with SCD and lower PK thermostability had significantly higher absolute reticulocyte counts (ARC, p<0.0001), lower hemoglobin (p=0.012) and HbF (p=0.020) levels and increased RBC adhesion to laminin (p=0.007). Furthermore, PK thermostability was significantly correlated with EImax (p=0.017) and inversely correlated with PoS (p=0.011) and P50 (p=0.003), indicating that patients with less stable RBC PK had less deformable RBCs which sickled at a higher oxygen tension. RBC adhesion to laminin was significantly correlated with both ARC (p=0.0003) and dense RBCs (p=0.019). To explore whether our findings were a reflection of reticulocytosis we fractionated whole blood samples of HbSS patients according to cell density. We found that more RBCs from the most dense fraction adhered to laminin than from the less dense, reticulocyte enriched, fraction, even though RBCs from this less dense fraction had reduced PK-thermostability. Additionally, the most dense RBCs had the lowest PK activity, were less deformable and had a higher PoS (data not shown). Altogether these findings indicate that the reduced PK thermostability we found in our SCD cohort is associated with an overall functionally impaired RBC population with increased RBC adhesion and ARC. We found no correlation of markers of RBC dehydration (Ohyper and % dense RBCs) with PK thermostability which suggests that RBCs with reduced PK thermostability are not more dehydrated. Discussion/conclusion: This study shows for the first time a significant correlation between PK thermostability in sickle RBCs and RBC functions, such as adhesion, deformability and oxygen affinity. Our results suggest that enhancing the activity and stability of PK, with PK activators, is an attractive target in SCD that might improve other pathophysiological targets outside RBC metabolism. Future studies are needed to explore how activation of PK will affect these altered sickle RBC properties in vivo.

Sequencing of the Lumbricus terrestris genome reveals degeneracy in its erythrocruorin genes

The erythrocruorin of Lumbricus terrestris (LtEc) is a relatively large macromolecular assembly that consists of at least four different hemoglobin subunits (A, B, C, and D) and four linker subunits (L1, L2, L3, and L4). The complexity and stability of this large structure make LtEc an attractive hemoglobin-based oxygen carrier that could potentially be used as a substitute for donated red blood cells. However, the sequences of the LtEc subunit sequences must be determined before a scalable recombinant expression platform can be developed. The goal of this study was to sequence the L. terrestris genome to identify the complete sequences of the LtEc subunit genes. Our results revealed multiple homologous genes for each subunit (e.g., two homologous A globin genes; A1 and A2), with the exception of the L4 linker. Some of the homologous genes encoded identical peptide sequences (C1 and C2, L1a and L1b), while cDNA and mass spectrometry experiments revealed that some of the homologs are not expressed (e.g., A2). In contrast, multiple sequences for the B, D, L2, and L4 subunits were detected in LtEc samples. These observations reveal novel degeneracy in LtEc and other annelids, along with some new revisions to its previously published peptide sequences.

Predicting Thalassemia Using Feature Selection Techniques: A Comparative Analysis.

Thalassemia represents one of the most common genetic disorders worldwide, characterized by defects in hemoglobin synthesis. The affected individuals suffer from malfunctioning of one or more of the four globin genes, leading to chronic hemolytic anemia, an imbalance in the hemoglobin chain ratio, iron overload, and ineffective erythropoiesis. Despite the challenges posed by this condition, recent years have witnessed significant advancements in diagnosis, therapy, and transfusion support, significantly improving the prognosis for thalassemia patients. This research empirically evaluates the efficacy of models constructed using classification methods and explores the effectiveness of relevant features that are derived using various machine-learning techniques. Five feature selection approaches, namely Chi-Square (χ2), Exploratory Factor Score (EFS), tree-based Recursive Feature Elimination (RFE), gradient-based RFE, and Linear Regression Coefficient, were employed to determine the optimal feature set. Nine classifiers, namely K-Nearest Neighbors (KNN), Decision Trees (DT), Gradient Boosting Classifier (GBC), Linear Regression (LR), AdaBoost, Extreme Gradient Boosting (XGB), Random Forest (RF), Light Gradient Boosting Machine (LGBM), and Support Vector Machine (SVM), were utilized to evaluate the performance. The χ2 method achieved accuracy, registering 91.56% precision, 91.04% recall, and 92.65% f-score when aligned with the LR classifier. Moreover, the results underscore that amalgamating over-sampling with Synthetic Minority Over-sampling Technique (SMOTE), RFE, and 10-fold cross-validation markedly elevates the detection accuracy for αT patients. Notably, the Gradient Boosting Classifier (GBC) achieves 93.46% accuracy, 93.89% recall, and 92.72% F1 score.

The anti-SARS-CoV-2 BNT162b2 vaccine suppresses mithramycin-induced erythroid differentiation and expression of embryo-fetal globin genes in human erythroleukemia K562 cells

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causative of the ongoing coronavirus disease 2019 (COVID-19) pandemic. The SARS-CoV-2 Spike protein (S-protein) plays an important role in the early phase of SARS-CoV-2 infection through efficient interaction with ACE2. The S-protein is produced by RNA-based COVID-19 vaccines, that were fundamental for the reduction of the viral spread within the population and the clinical severity of COVID-19. However, the S-protein has been hypothesized to be responsible for damaging cells of several tissues and for some important side effects of RNA-based COVID-19 vaccines. Considering the impact of COVID-19 and SARS-CoV-2 infection on the hematopoietic system, the aim of this study was to verify the effect of the BNT162b2 vaccine on erythroid differentiation of the human K562 cell line, that has been in the past intensively studied as a model system mimicking some steps of erythropoiesis. In this context, we focused on hemoglobin production and induced expression of embryo-fetal globin genes, that are among the most important features of K562 erythroid differentiation. We found that the BNT162b2 vaccine suppresses mithramycin-induced erythroid differentiation of K562 cells. Reverse-transcription-qPCR and Western blotting assays demonstrated that suppression of erythroid differentiation was associated with sharp inhibition of the expression of α-globin and γ-globin mRNA accumulation. Inhibition of accumulation of ζ-globin and ε-globin mRNAs was also observed. In addition, we provide in silico studies suggesting a direct interaction between SARS-CoV-2 Spike protein and Hb Portland, that is the major hemoglobin produced by K562 cells. This study thus provides information suggesting the need of great attention on possible alteration of hematopoietic parameters following SARS-CoV-2 infection and/or COVID-19 vaccination.

Inhibitory effects of SARS-CoV-2 spike protein and BNT162b2 vaccine on erythropoietin-induced globin gene expression in erythroid precursor cells from patients with β-thalassemia

During the recent coronavirus disease 2019 (COVID-19) pandemic several patients with β-thalassemia have been infected by severe acute respiratory syndrome coronavirus (SARS-CoV-2), and most patients were vaccinated against SARS-CoV-2. Recent studies demonstrate an impact of SARS-CoV-2 infection on the hematopoietic system. The main objective of this study was to verify the effects of exposure of erythroid precursor cells (ErPCs) from patients with β-thalassemia to SARS-CoV-2 spike protein (S-protein) and the BNT162b2 vaccine. Erythropoietin (EPO)-cultured ErPCs have been either untreated or treated with S-protein or BNT162b2 vaccine. The employed ErPCs were from a β-thalassemia cellular Biobank developed before the COVID-19 pandemic. The genotypes wereβ+-IVSI-110/β+-IVSI-110 (one patient), β039/β+-IVSI-110 (3 patients), and β039/β039 (2 patients). After treatment with S-protein or BNT162b2 for 5 days, lysates were analyzed by high performance liquid chromatography (HPLC), for hemoglobin production, and isolated RNA was assayed by RT-qPCR, for detection of globin gene expression. The main conclusions of the results obtained are that SARS-CoV-2 S-protein and BNT162b2 vaccine (a) inhibit fetal hemoglobin (HbF) production by β-thalassemic ErPCs and (b) inhibit γ-globin mRNA accumulation. In addition, we have performed in silico studies suggesting a high affinity of S-protein to HbF. Remarkably, the binding interaction energy of fetal hemoglobin to S-protein was comparable with that of angiotensin-converting enzyme 2 (ACE2). Our results are consistent with the hypothesis of a relevant impact of SARS-CoV-2 infection and COVID-19 vaccination on the hematopoietic system.

Effect of hydroxyurea on SP1, LIN28B, IGF2BP3, COL4A5, BCL2, gamma globin genes expression: an in vitro study

BackgroundIn some β-thalassemia intermedia patients, hydroxyurea (HU) increases hemoglobin and HbF levels. However, HUs’ effects molecular mechanism is still unclear.MethodsIn this study, a weighted gene co-expression network analysis was conducted on the GSE109186 dataset. The genes LIN28A, COL4A5, SP1, BCL2, and IGF2BP3 were identified as hub genes involved in the γ-gene switching process. The effect of HU treatment at doses of 50, 100, and 150 μM for 12, 24, and 48 h on the K562 cell line was examined by using qRT-PCR to measure the expression levels of these hub genes.ResultsSP1 gene expression decreased after treatment with 50, 100, and 150 μM HU for 12, 24, and 48 h. The expression of the LIN28A gene was tripled at three concentrations of 50, 100, and 150 μM for 12 h. The IGF2BP3 gene expression was doubled after 24 and 48 h at a concentration of 150 μM HU. Regarding COL4A5 gene expression, except at 12 h after treatment at a concentration of 50 μM, a significant increase was observed in other concentrations and times. The BCL2 gene expression pattern at all concentrations decreased significantly after 12 h. The γ gene showed a significant increase compared to the control group after 24 and 48 h at the different concentrations.ConclusionThe results showed that in HU-treated cells, changes in the expression of LIN28A, COL4A5, SP1, and IGF2BP3 genes were accompanied by an increase in γ-gene expression. By elucidating precisely the mechanism of γ-to-β gene switching, we can hope for less complicated drugs.

Comparison of Evolutionary Relationships between Branchiostoma floridae, Ciona intestinalis, and Homo sapiens Globins Provide Evidence of Gene Co-Option and Convergent Evolution.

Globins have been studied as model proteins to elucidate the principles of protein evolution. This was achieved by understanding the relationship between amino acid sequence, three-dimensional structure, physicochemical properties, and physiological function. Previous molecular phylogenies of chordate globin genes revealed the monophyletic evolution of urochordate globins and suggested convergent evolution. However, to provide evidence of convergent evolution, it is necessary to determine the physicochemical and functional similarities between vertebrates and urochordate globins. In this study, we determined the expression patterns of Ciona globin genes using real-time RT-PCR. Two genes (Gb-1 and Gb-2) were predominantly expressed in the branchial sac, heart, and hemocytes and were induced under hypoxia. Combined with the sequence analysis, our findings suggest that Gb-1/-2 correspond to vertebrate hemoglobin-α/-β. However, we did not find a robust similarity between Gb-3, Gb-4, and vertebrate globins. These results suggested that, even though Ciona globins obtained their unique functions differently from vertebrate globins, the two of them shared some physicochemical features and physiological functions. Our findings offer a good example for understanding the molecular mechanisms underlying gene co-option and convergence, which could lead to evolutionary innovations.

Selective Globin Gene Regulation By the Non-Canonical Baf Chromatin Remodeling Complex

The regulation of the beta-type globin genes has served as a powerful model for developmental transcriptional control, with humans expressing embryonic (HBE), two fetal (HBG1/2) and two adult (HBB and HBD) versions at the corresponding developmental stages. Reactivation of HBG in adult erythroid cells is of benefit to patients with sickle cell disease and β-thalassemia. While past efforts focused on the identification of repressors of the HBG genes, including BCL11A, ZBTB7A, and NFI-A/X, to date no transcriptional activators have been identified with selectivity for any of the globin genes. Using a CRISPR-Cas9 screen in the HUDEP2 erythroid cell line, we recently identified BRG1/SMARCA4 as a potential activator of HBG production. BRG1 is a core ATPase component of the multi-subunit BAF (BRG1/BRM-associated factor) complex; different subtypes of this large chromatin remodeler family are specific to particular cell types or developmental stages. BRG1 was previously implicated in globin gene regulation but its molecular composition and whether it has selectivity for any of the genes in the cluster is unknown. Notably, we found that loss of BRG1 in both HUDEP2 and primary erythroid cells impairs transcription of HBG to a much greater extent than that of HBB. Here we functionally dissected BAF subunits to decipher composition of the relevant BAF complex and the mechanism for this unexpected HBG gene selectivity. We used CRISPR-Cas9 in HUDEP2 cells and human primary erythroid cultures to test the requirement for 14 different BAF subunits for selective HBG transcription. Among these, the BAF60A component emerged as critically required for the normal production of HBG but not HBB in HUDEP2 cells. Depletion of BAF60A in human primary erythroid cultures reduced HBG by up to 80% with no reduction in HBB as assessed by western blot, flow cytometry, HPLC, RT-PCR, and droplet digital RT-PCR. We also observed a reduction in HBD expression, suggesting that BAF60A functions in a gene selective manner but not necessarily favoring the fetal over the adult-type globin genes. α-type globin genes were unaffected by BAF60A loss, further demonstrating the gene selectivity of BAF60A action. RNA-seq of BAF60A-targeted cells showed that the most downregulated transcripts were from the two HBG genes and the BGLT3 long non-coding RNA, which typically parallels HBG in expression. These results revealed an unexpected gene selectivity of the BAF complex, conveyed at least in part by BAF60A. To assess global chromatin accessibility upon BAF60A loss in primary erythroid cells we utilized ATAC-seq. Among ~132,000 accessibility peaks, ~10,000 were reduced in BAF60A targeted cells. Interestingly, we saw a strong decrease in chromatin accessibility at the HBG and HBD genes with minimal to no effect on the HBB or α-globin genes, in line with gene expression data, again reflecting the gene specificity of BAF60A. BAF60A can be found in different classes of BAF complexes, but is absolutely required for the non-canonical BAF (ncBAF) subtype. ncBAF is a relatively recently described BAF complex that is distinguished from other classes of BAF complexes by the presence of the bromodomain protein BRD9. Therefore, we hypothesized that ncBAF is the relevant BAF complex required for selective HBG transcription. Genetic or pharmacologic disruption of BRD9 in HUDEP2 cells recapitulated the BAF60A phenotype, with decreased HBG and HBD expression but sparing of the HBB and α-globin genes. This is the first study of the role of the non-canonical BAF complex in hemoglobin gene regulation. Our results demonstrate remarkable selectivity of this subtype of a broadly active chromatin remodeling complex for specific hemoglobin genes in adult erythroid cells. Further work on the ncBAF complex will focus on rerouting the BAF complex to promote the transcription of HBG and HBD in hemoglobinopathies.

Genome-Scale CRISPR-Cas12a Screen Identifies Novel Fetal Hemoglobin Regulators

Reversal of the postnatal hemoglobin switch in red blood cells is a promising approach to therapies for sickle cell disease and β-thalassemia, as reactivating fetal hemoglobin (HbF, α2γ2) in adult red blood cells ameliorates disease complications. Studies over several decades have illuminated the paradigm of this fetal-to-adult hemoglobin transition, including central roles of transcriptional repressors BCL11A, LRF, and NFIA/X, which recruit repressive chromatin modifiers to the γ-globin locus. To elucidate undescribed regulatory mechanisms of these molecules and reveal new targets for therapies, we performed the first genome-wide genetic screen to pinpoint specific pathways or protein complexes that regulate HbF expression in adult erythroid cells. Because Cas9 technology is limiting at the genome-wide scale, we conducted a CRISPR-Cas12a genetic screen targeting all known coding genes in the human genome using a novel custom array directed towards 18,292 genes. The single CRISPR RNA (crRNA) library was cloned into a lentivirus scaffold and transduced into the adult-type erythroid cell line, HUDEP2, engineered to stably express Cas12a. HUDEP2 cells express little HbF, allowing for positive phenotypic selection (HbF+) by fluorescence-activated cell-sorting. By isolating the top 10% and bottom 10% of HbF-expressing cells and determining the representation of crRNAs via deep sequencing, we identified a crRNA subset enriched in the high-HbF population encompassing 211 candidate genes, representing potential regulators of HbF. To prioritize these genes for follow up studies, we conducted a domain-focused, CRISPR-Cas9 screen of all 211 candidate genes. Using 2,184 sgRNAs, this validation Cas9 screen in HUDEP2 cells nominated 18 high-confidence targets. Two of the top candidate genes were identified as modulators of the phosphatase PP2A, PPP2R4 and TIPRL. PP2A is a multi-subunit complex with diverse cellular functions as a serine/threonine phosphatase. To our knowledge, it has no previously known role on globin gene production. In validation experiments, disruption of either PPP2R4 or TIPRL in HUDEP2 cells significantly increased γ-globin mRNA and protein expression. Using sgRNA-Cas9 ribonucleoprotein complex nucleofection, PPP2R4 gene editing in primary human CD34+ cell derived erythroblasts significantly increased γ-globin mRNA and protein expression without overtly affecting erythroid maturation. Notably, the degree of effect is similar to that of BCL11A +58 enhancer disruption. Depletion of either PP2A regulator in HUDEP2 cells resulted in markedly reduced BCL11A protein levels. Furthermore, BCL11A overexpression in PPP2R4 or TIPRL-targeted cells reduced γ-globin mRNA commensurate to parental control cells, thereby demonstrating both TIPRL and PPP2R4 mediate γ-globin silencing predominantly via BCL11A. RNA-sequencing of TIPRL and PPP2R4-edited HUDEP2 cells revealed strong overlap of differentially expressed genes, consistent with convergent function. Altogether, our studies utilizing a novel Cas12a-based, genome-wide screen nominate a new pathway mediating γ-globin silencing via regulation of BCL11A.

Direct and Indirect Functions of TR4 in the Control of Fetal Hemoglobin Silencing

Elevated levels of fetal hemoglobin (HbF) compensate for reduced normal β-globin chains and ameliorate clinical symptoms for patients with beta-globinopathies, such as sickle cell disease (SCD). The embryonic and fetal globin genes, but not the adult β-globin gene, have direct repeat (DR) elements in their promoters, which have been implicated in γ-globin gene repression (Tanabe et al., 2002). We previously purified a DR element-binding protein complex, which we named DRED, and was the first identified HBG gene repressor (Tanabe et al., 2002). DRED activity is conferred by a complex including LSD1, recruited by the nuclear receptors TR2/TR4 (Cui et al., 2011). BCL11A is a well-characterized transcription factor that independently represses the γ-globin genes through binding to their promoters (Liu et al., 2018). We have shown by co-immunoprecipitation that TR4 interacts with BCL11A in HUDEP2 cells. To understand how TR4 acts to repress the γ-globin gene and the relationship of TR4 to BCL11A in γ-globin repression, we characterized the chromatin occupancy of TR4 and BCL11A within the β-globin locus by CUT&RUN (CNR) in HUDEP2 cells. We established HUDEP2 cells bearing TR4 tagged with 3FLAG+3Myc epitopes (FM-TR4) and in the same cells, BCL11A tagged with 3HA+3Myc (HM-BCL11A) epitopes by genome editing. In addition, another HUDEP2 cell line bearing BCL11A tagged with the 3HA+3Myc (HM-BCL11A) epitope as well a cell line bearing TR4 tagged with the 3FLAG+3Myc epitopes (FM-TR4) were generated. The tagged cell lines not only improved the efficiency of antibody targeting, but also facilitated direct comparison of TR4 vs BCL11A chromatin occupancy by binding of the common Myc epitope in FM-TR4 and HM-BCL11A cell lines. Unbiased motif discovery of TR4 CNR binding of these epitopes in all 3 cell lines yielded the motif of a direct repeat consisting of 2 AGGTCA repeat elements with a 1 nt spacer. The exact match of BCL11A motif with one of the direct repeat elements of TR4 motif suggested that BCL11A and TR4 may be compete for binding to the γ-globin promoter. Overall, TR4 and BCL11A showed a similar pattern of occupancy within the globin locus, although of lower intensity. TR4 presented strong interaction with the locus control regions, among which HS2 and HS3 were the highest, consistent with the model of long-distance interaction through chromosomal looping. However, TR4 was found to be significantly less occupied at the γ-globin promoters than BCL11A. To test whether TR4 and BCL11A can bind in vitro to the motifs found in the γ-globin promoters, we performed TR4 and BCL11A electrophoretic mobility shift assays (EMSAs). We showed that TR4 binds to the DR1 element within the γ-globin promoters, which contains the distal TGACCA motif that was bound by BCL11A. Notably, mutation of the TGACCA motif disrupted both BCL11A and TR4 binding, while the other direct motif is indispensable for TR4 binding, supporting overlapping binding of BCL11A and TR4. Interestingly, DNA-TR4 protein complexes were competitively depleted by high concentrations of BCL11A and vice versa, suggesting competitive binding between the two factors. Studies of this mechanism in the erythroid cells are underway. In addition, unbiased motif discovery of TR4 CNR also enriched for KLF1, LRF and NF-Y motifs. Co-IP assays demonstrated interaction between TR4 and KLF1 and LRF, suggesting the presence of a large repressor complex. We also explore genome-wide occupancy of TR4 and discovered strong TR4 interactions at promoters of multiple HbF repressing transcription factors and corepressors, including NFIA and EHMT1, suggesting that the role of TR4 in HbF repression may be partially mediated by regulating expression of various HbF repressor genes. In summary, these data suggest that the function of TR4 in HbF silencing is mediated in part by direct repression of HBG promoters in a competitive manner with BCL11A, and in part by regulating the expression of multiple HbF repressor genes.

Ncrna-a3 Epigenetically Regulates TAL1 and Its Target Genes to Drive Erythroid Differentiation

Erythropoiesis is the development of enucleated red blood cells from multipotent hematopoietic stem cells. This complex process is tightly regulated by the dynamic changes in occupancy of tissue specific transcription factors (TFs) that activate and repress genes appropriately. TAL1, a critical regulator is expressed throughout the development of mature erythroblasts from multi-progenitors. Loss of TAL1 leads to defective erythropoiesis. As opposed to TAL1's role in erythropoiesis, itis an extraneous factor in developing lymphoid cells and aberrant expression of TAL1 in T-cells is associated with T-ALL. The differential regulation during normal and malignant hematopoiesis remains largely unclear. We found that a distil RNA - ncRNA-a3, is transcribed from erythroid specific enhancer, 50kbp downstream of the TAL1 TSS. We hypothesized that ncRNA-a3 plays an important role in regulating TAL1 and its target gene transcription in an erythroid specific manner. To test this hypothesis, we examine the regulatory potential of ncRNA-a3 towards the activation of TAL1 expression in the context of hematopoiesis and leukemogenesis. We used RNA interference to deplete ncRNA-a3 expression across several hematopoietic and leukemic cells. The decrease in ncRNA-a3 resulted in significant reduction of TAL1 transcript and protein levels in hematopoietic cells while TAL1 transcripts showed little or no reduction in leukemic cells. Subsequently, transcriptomic profile changes in erythroleukemic K562 cells showed downregulation of erythroid specific targets of TAL1. To ascertain the role of ncRNA-a3 in erythropoiesis, we used siRNA against ncRNA-a3 in primary CD34+ cells and subjected cells to differentiation. Quantification of early and late erythroblasts by colony forming assay and flow cytometry indicated impaired erythroid differentiation and maturation in orthochromatic and polychromatic stages. Further, RNA-seq analysis of ncRNA-a3 knockdown cells revealed defects in globin gene function, heme biosynthesis and nucleosome condensation compared to control CD34+ cells during time course EPO induced erythroid differentiation. Mechanistically, we observed ncRNA-a3s occupancy at TAL1 regulatory regions from ChIRP-qPCR across TAL1 locus. NG Capture-C data depicting changes in interaction frequencies indicated that ncRNA-a3 maintains canonical interactions at the TAL1 locus. Knockdown of ncRNA-a3 negatively impacted the chromatin accessibility in TAL1 and TAL1 target loci. Perturbation of chromatin landscape affected TAL1 and TAL1 binding partner - P300 and BRG1 occupancy at TAL1 target sites. To distinguish reduced TAL1 binding as a consequence of lower levels of TAL1, from RNA dependent binding of TAL1, we examined TAL1, P300 and BRG1 chromatin occupancy through Cut&Run in conjunction with RNase treatment. Effective depletion of global RNAs resulted in reduced enrichment of TAL1, P300 and BRG1 bound fragments indicating possible RNA dependent binding of TAL1 and its cofactors. TAL1 coimmunoprecipitation using RNase treatment (1) and ncRNA-a3 KD (2), demonstrated that TAL1s interaction with P300 and BRG1 is RNA dependent, but ncRNA-a3 independent. RNA-IP results further confirmed that ncRNA-a3 is associated with TAL1 through its interacting epigenetic cofactors P300 and BRG1. Together, our data indicate that although RNA dependent binding of TAL1 and its epigenetic cofactors is cell type or target locus specific, ncRNA-a3 modulates the occupancy of TAL1, P300 and BRG1 at the TAL1 locus during erythroid specific TAL1 transcription.